[BioC] nested model: lme, aov and LSMeans

[shirley zhang]

Dear all,

I'm working with a nested model (mixed).

I have four factors: Patients, Tissue, sex, and tissue_stage.

Totally I have 10 patients, for each patient, there are 2 tissues
(Cancer vs. Normal).

I think Tissue and sex are fixed. Patient is nested in sex,Tissue is
nested in patient,  and tissue_stage is nested in Tissue.


I tried aov and lme as the following,

> aov(gene ~ tissue + gender + patients%in%gender + stage%in%tissue
>lme(gene ~ tissue + gender, random = list(patients = ~1 , stage = ~ 1))


I got results from aov, but I got error message from lme which is
false convergence (8). so I could not compare the results of aov with
lme.

Could anybody tell me whether I use the correct command? How can I get
LSMeans for Cancer vs. Normal in R ( I know it is easy in SAS)?

Thanks,
Shirley